Proteopedia:What's New

What's New in Proteopedia? This page lists new pages, substantially updated pages, and new capabilities within Proteopedia. In contrast, Proteopedia:News lists external news such as adoptions, blogs, press, meetings, seminars and workshops about Proteopedia.

A major purpose of this page is to make it easier for users to find out about new user-created pages with substantial content. Only user-created pages that have substantial content (at least one paragraph of user-added text with three or more green links), and that are reasonably complete should be listed below. Pages that are started, but not yet completed, should not be listed until they are reasonably complete. Automatically seeded new pages, titled with PDB codes, are not listed here. Minor updates to existing pages should not be listed. Please add new items at the top. If a linked page is not new, but has been updated with substantial new content, please say so. Each page's history tab (at the top) shows when it was created and the date of each update. The left arrow symbol (<-) signifies a page that redirects to another page. Because this page is maintained manually, the lists for recent months are usually incomplete. There are typically other new articles that are not yet listed. You may also wish to consult Topic pages (also maintained manually); Special:Newpages which is automatically generated, but includes the pages for new PDB entries seeded by the OCA robot; or all pages whose titles do not begin with a numeral (thus excluding pages titled with PDB codes, but not limited to new pages).

May, 2011

 * RNase A
 * RNase A Oligomers
 * RNase A NMR
 * RNaseA Nobel Prizes
 * RNaseS RNaseB

April, 2011

 * CASP
 * Homology modeling
 * Homology modeling servers

March, 2011

 * Lac repressor has been updated to incorporate new understanding of interactions of proteins with the minor groove of DNA.
 * Nitrotyrosine, a post-translational modification occurring in inflammation that often inactivates enzymes.
 * Java

October, 2010

 * Psi and Phi Angles, Identifies the atoms which make up these angles, illustrates how Jmol can be used to determine their values and by drawing planes illustrates how their values are set by rotating the plane of the peptide bonds and the alpha-carbons and the atoms bonded to them.

July, 2010

 * Glutamate Receptor

June, 2010

 * Metal-Ligand Polyhedra: Mixtures of certain metal ions with bent bidentate ligands self-assemble into large polygons that can be functionalized to serve as receptors, nanoreactors, etc.

May, 2010

 * Rhodopsin

April, 2010

 * Green Fluorescent Protein, significant additions have been made to this page.
 * NADPH Cytochrome P450 Oxidoreductase
 * Proteopedia:Twitter - Proteopedia is now on Twitter. Follow us at Proteopedia on Twitter.
 * The pore forming toxin, &#945;-hemolsyin

March, 2010

 * Serine Proteases: A Tutorial of Chymotrypsin, Trypsin and Elastase, examines the structural basis of specificity and a general properties of the catalytic mechanism

January, 2010

 * Archaeal Histones, illustrates the structural features of two histones and a dimer of one of them.
 * Syn and anti nucleosides, illustrates the structural differences in the syn and anti configurations of nucleosides.
 * Ramachandran Plots, this page is a copy of User:Karl Oberholser/Ramachandran Plots which is a protected page.
 * Escherichia coli LepA, the ribosomal back translocase

December, 2009
This month's list is incomplete:
 * Interactions between Antibiotics and the Ribosome
 * Large Ribosomal Subunit of Haloarcula marismortui
 * Azithromycin bound to the Large Ribosomal Subunit of Haloarcula
 * Reverse transcriptase

November, 2009
This month's list is incomplete:
 * RecG in complex with a synthetic three-way DNA junction resembling a stalled replication fork
 * DExD/H-box RNA-dependent ATPase DDX19 in the open and closed cleft conformation

October, 2009
This month's list is incomplete:
 * Ribosome, also featured at the Main Page, since its structures won the Nobel Prize in Chemistry this month!
 * Intrinsically Unfolded Proteins (IUP)
 * Extremophiles
 * Proteopedia:Guidelines for Ethical Writing

July, 2009
This month's list is incomplete:
 * Influenza hemagglutinin
 * The 21st and 22nd amino acids were added to Amino Acids: namely Selenocysteine and Pyrrolysine.

March, 2009
This month's list is incomplete:
 * Mechanosensitive channels: opening and closing includes morphs of the ion-conducting channel opening and closing.
 * High school teachers' resources
 * Richards, Frederic M. (1925-2009) including a photo of "Fred's Folly".

February, 2009
This month's list is incomplete:
 * Ion channels is an attempt to cover a family of proteins and list their available PDB structures.

January, 2009
This month's list is incomplete:

December, 2008

 * Conservation, Evolutionary now includes instructions on how to show a ConSurf result as a scene in Proteopedia, complete with the standard ConSurf color key.
 * Resolution now includes a movie illustrating the relation between the atomic model and the electron density map while resolution ranges from 0.5 to 5.0 &Aring;ngstroms.

November, 2008

 * RNA silencing: suppression by viruses. Concerns the research awarded the 2006 Nobel Prize in Physiology or Medicine. Linked are new pages on specific RNA silencing proteins: Plant viral protein p19, Tomato aspermy virus protein 2b, and Flock house virus B2 protein.
 * Transcription Termination Factor Rho.
 * Mechanosensitive ion channel of large conductance, with open, intermediate, and closed conformations, 2oar.
 * Crucial role of electrostatic features in halotolerance of carbonic anhydrase, 1y7w.
 * Hydrogen in macromolecular models
 * Molecular modeling and visualization software, whick links to new pages on PyMOL, Jmol, RasMol, and Chime.

October, 2008

 * Lac repressor structure, including a morph of the DNA-binding domain bending the operator DNA.
 * Poly(A) Polymerase, 2q66: A new section complementing this month's article in Molecule of the Month.
 * Structure Gallery Generator generates galleries of thumbnail molecular images, linked to Proteopedia, for external websites or within Proteopedia pages.
 * Acetylcholinesterase in complex with anti-Alzheimer's drug candidates: Crystal packing mediates enantioselective ligand recognition, 1zgb.
 * Thermal stability analysis of alcohol dehydrogenase: 2oui, 2nvb.
 * Confirmation of a heterodimer predicted by computational genomic analysis (neither chain could be crystallized alone): 2g38.
 * Complex Of S. griseus Proteinase B And Polypeptide Chymotrypsin Inhibitor-1 From Russet Burbank Potato Tubers, 4sgb.
 * Structures Saving the Most Lives is a new list added to the Highest impact structures page originally created in February, 2008.
 * Hydrogen bonds
 * Nobel Prizes for 3D Molecular Structure
 * Morphs: Although this page was created in March, 2008, most of its content was added this month.
 * Proteopedia: Email list
 * What's New in Proteopedia? (this page).
 * Several pages about visualization software: FirstGlance in Jmol, Swiss-PDBViewer = DeepView, and Protein Explorer.

September, 2008

 * Anticancer Prodrug CPT-11 complexed with Torpedo californica Acetylcholinesterase 1u65
 * Avian Influenza Neuraminidase, Tamiflu and Relenza
 * Insecticidal delta-endotoxin Cyt2Ba from Bacillus thuringiensis.
 * TEM1-β-Lactamase/ β-Lactamase Inhibitor Protein (BLIP), 2b5r and 1s0w.
 * Acid-beta-glucosidase covalently bound to conduritol B epoxide, 1y7v.
 * Ribonuclease A, 1rta has a new section complementing this month's article in Molecule of the Month.
 * DRuMS, standard color schemes for macromolecules, and color key templates for use in Proteopedia.
 * Glutamine Synthetase, which includes instructions on how to use the Jmol console for advanced scene authoring.

August, 2008

 * HIV-1 protease
 * Pyruvate phosphate dikinase with a morph of the catalytic reaction and conformational changes.
 * Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System with a morph of the catalytic reaction and conformational changes.
 * Antizyme Inhibitor
 * Selenocysteine Synthase, SelB Recognition is a new page complementing this month's article in Molecule of the Month.
 * Teaching Strategies Using Proteopedia‎
 * Protein structure lesson plan for BioSci 203
 * Proteopedia: News

July, 2008

 * Biotin Protein Ligase
 * YAGE, A Prophage Protein Belonging To The Dihydrodipicolinic Acid Synthase Family From E. Coli K12, 2v9d.
 * Ramachandran Plots
 * Flexibility of aromatic residues in acetylcholinesterase
 * Horizontal gene transfer ssDNA binding protein from Agrobacterium tumefaciens VirE1/VirE2=3btp
 * Proteopedia:Page of the Year Competition
 * Student Projects

June 2008

 * Computational design of a Kemp elimination catalyst 2rkx.
 * Recoverin, a calcium-activated myristoyl switch‎
 * G protein, ras oncogene: James_D_Watson/Proteins_Intro.
 * Ribulose-1,5-bisphosphate carboxylase/oxygenase uses the Kinemage applet.
 * Acid-beta-glucosidase
 * Rop protein


 * Institute of Clinical Biochemistry, Oslo, Norway.
 * Research Groups <- Institutes
 * Teaching Scenes, Tutorials, and Educators' Pages‎

About Macromolecular Structure
 * About Macromolecular Structure <- About Protein Structure
 * Amino Acids
 * Asymmetric Unit
 * Atomic coordinate file
 * Biological Unit <- Quaternary structure
 * Free R
 * NMR Ensembles of Models‎
 * PDB identification code
 * Quality assessment for molecular models
 * R value
 * Resolution
 * Temperature value <- Disorder, B value
 * Unit cell

May 2008

 * Acetylcholinesterase
 * 2ace with an overview of the significance of this, the first acetylcholinesterase structure.
 * Anti-Alzheimer's drug, Aricept, complexed with acetylcholinesterase 1eve.
 * Tacrine Binding To Aromatic Residues In The Active-site Gorge Of Acetylcholinesterase, 1acj.
 * Serum Paraoxonase-1 (PON1) via directed evolution 1v04.
 * Human acid-beta-glucosidase, 1ogs.
 * Photosystem II, an undergraduate project.
 * Ozonolysis: cool animation of a chemical reaction!


 * Help:Copying FirstGlance Scenes into Proteopedia

April 2008

 * Acetylcholinesterase inhibited by nerve agent soman 1som.
 * Highest resolution acetylcholinesterase so far, 1ea5.
 * Tetramerization domain of acetylcholinesterase 1vzj.
 * Locations of mutations in oncogene phosphatidylinositol 3-kinase 2rd0, with many of the published figures made interactive in Jmol.
 * Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, 2ic8.
 * Major Histocompatibility Complex Class I (no Jmol yet)
 * Personal favorites
 * Believe It or Not!
 * Help:Protected Pages

March 2008

 * Conformational flexibility in the peripheral site of Torpedo californica acetylecholinesterase revealed by the complex structure with a bifunctional inhibitor, 2cek.
 * Proton Channels
 * Proteopedia:Namespaces
 * Proteopedia:About
 * SGAP Streptomyces griseus Aminopeptidase (SGAP) (no Jmol)

February 2008

 * Hemoglobin
 * Highest impact structures of all time.
 * Nucleosomes
 * Scorpion alpha-toxin 1qlh.
 * Peptide
 * Proteopedia:Problems
 * Personal favorites

January 2008

 * AChE inhibitors and substrates
 * Dihydrofolate reductase

October-December 2007

 * Serine Protease
 * Nqo1 NADH quinone oxidoreductase (NQO1) in complex with its potent inhibitor dicoumarol.
 * 1xjo S. griseus aminopeptidase.
 * Glycine
 * Bacterial Intein-Like Domains (BILs) (no Jmol, no green links)
 * Hint auto-proteolytic protein-processing domains (no Jmol, no green links)